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PMC:7556165 / 62166-63571 JSONTXT

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LitCovid-sample-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T175 997-1004 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T176 1044-1051 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T177 1071-1078 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T178 1119-1126 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080

LitCovid-sample-sentences

Id Subject Object Predicate Lexical cue
T373 0-118 Sentence denotes The molecular mechanisms involved in the cytokine storm and the role of ACE2 are currently still not fully understood.
T374 119-332 Sentence denotes As discussed above, virus binding to the ACE2 is the event that initiates viral replication in susceptible cells, such as alveolar epithelial cells, vascular cells and immune system cells (macrophages, monocytes).
T375 333-461 Sentence denotes This has been suggested to trigger the primary inflammatory response, which involves apoptosis and pyroptosis (Fu et al., 2020).
T376 462-712 Sentence denotes The apoptosis pattern indices cell death to avoid viral replication in the absence of overt inflammation, whereas, pyroptosis is a violent form of programmed cell death, followed by an inflammatory storm (Cookson and Brennan, 2001; Liu et al., 2016).
T377 713-959 Sentence denotes In the standard pyroptosis model, when the pathogen enters the host cell, some specific structures on the pathogen surface (PAMPs–pathogen associated molecular patterns) are identified by pattern recognition receptors (PRRs) on the host membrane.
T378 960-1405 Sentence denotes One common PRR is NOD-like receptors protein 3 (NLRP3), which forms together with a protein caspase activating protein (ASC or apoptosis-associated speck-like protein containing a caspase recruitment domain) and pro-caspase 1, the inflammasome unit capable of recruiting proinflammatory cytokines and inducing cell lysis with further inflammation signals (Fernandes-Alnemri et al., 2007; Schroder and Tschopp, 2010; Wree et al., 2014; Figure 9).

LitCovid-sample-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T144 287-300 Body_part denotes immune system http://purl.obolibrary.org/obo/UBERON_0002405

LitCovid-sample-Pubtator

Id Subject Object Predicate Lexical cue pubann:denotes
1725 72-76 Gene denotes ACE2 Gene:59272
1726 160-164 Gene denotes ACE2 Gene:59272
1727 1008-1013 Gene denotes NLRP3 Gene:114548
1728 1176-1185 Gene denotes caspase 1 Gene:834
1729 950-958 Gene denotes membrane Gene:43740571
1730 554-566 Disease denotes inflammation MESH:D007249
1731 1294-1306 Disease denotes inflammation MESH:D007249

LitCovid-sample-UniProt

Id Subject Object Predicate Lexical cue uniprot_id
T5872 72-76 Protein denotes ACE2 https://www.uniprot.org/uniprot/Q9UFZ6
T5873 160-164 Protein denotes ACE2 https://www.uniprot.org/uniprot/Q9UFZ6
T5874 997-1006 Protein denotes protein 3 https://www.uniprot.org/uniprot/Q9JGT9|https://www.uniprot.org/uniprot/Q98663|https://www.uniprot.org/uniprot/Q8V3T9|https://www.uniprot.org/uniprot/Q6UBL8|https://www.uniprot.org/uniprot/Q6Q1S1|https://www.uniprot.org/uniprot/Q6E0W9|https://www.uniprot.org/uniprot/Q68Y30|https://www.uniprot.org/uniprot/Q5GA88|https://www.uniprot.org/uniprot/Q3LZX0|https://www.uniprot.org/uniprot/Q3I5J4|https://www.uniprot.org/uniprot/Q12988|https://www.uniprot.org/uniprot/Q0Q474|https://www.uniprot.org/uniprot/Q02967|https://www.uniprot.org/uniprot/Q00967|https://www.uniprot.org/uniprot/P09522|https://www.uniprot.org/uniprot/P05398|https://www.uniprot.org/uniprot/P03553|https://www.uniprot.org/uniprot/P03552|https://www.uniprot.org/uniprot/P03551
T5893 1042-1051 Protein denotes a protein https://www.uniprot.org/uniprot/Q38365|https://www.uniprot.org/uniprot/P25244|https://www.uniprot.org/uniprot/P25243|https://www.uniprot.org/uniprot/P15966|https://www.uniprot.org/uniprot/P09676|https://www.uniprot.org/uniprot/P07394|https://www.uniprot.org/uniprot/P03632|https://www.uniprot.org/uniprot/P03610|https://www.uniprot.org/uniprot/O64306
T5902 1052-1059 Protein denotes caspase https://www.uniprot.org/uniprot/Q9VAH1|https://www.uniprot.org/uniprot/O01382
T5904 1080-1083 Protein denotes ASC https://www.uniprot.org/uniprot/P50427|https://www.uniprot.org/uniprot/P15589|https://www.uniprot.org/uniprot/P08842|https://www.uniprot.org/uniprot/B2RA47
T5908 1140-1147 Protein denotes caspase https://www.uniprot.org/uniprot/Q9VAH1|https://www.uniprot.org/uniprot/O01382
T5910 1176-1185 Protein denotes caspase 1 https://www.uniprot.org/uniprot/Q9W1N0|https://www.uniprot.org/uniprot/Q9UCN3|https://www.uniprot.org/uniprot/Q9TV13|https://www.uniprot.org/uniprot/Q9N2I1|https://www.uniprot.org/uniprot/Q9MZV7|https://www.uniprot.org/uniprot/Q9MZV6|https://www.uniprot.org/uniprot/Q6PI75|https://www.uniprot.org/uniprot/Q6GSS3|https://www.uniprot.org/uniprot/Q6DMQ1|https://www.uniprot.org/uniprot/Q53EY6|https://www.uniprot.org/uniprot/P89116|https://www.uniprot.org/uniprot/P43527|https://www.uniprot.org/uniprot/P29466|https://www.uniprot.org/uniprot/P29452|https://www.uniprot.org/uniprot/O02002|https://www.uniprot.org/uniprot/B5MDZ1

LitCovid-sample-PD-IDO

Id Subject Object Predicate Lexical cue
T238 139-144 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T239 199-210 http://purl.obolibrary.org/obo/IDO_0000608 denotes replication
T240 214-225 http://purl.obolibrary.org/obo/IDO_0000467 denotes susceptible
T241 226-231 http://purl.obolibrary.org/obo/CL_0000000 denotes cells
T242 261-266 http://purl.obolibrary.org/obo/CL_0000000 denotes cells
T243 277-282 http://purl.obolibrary.org/obo/CL_0000000 denotes cells
T244 301-306 http://purl.obolibrary.org/obo/CL_0000000 denotes cells
T245 492-496 http://purl.obolibrary.org/obo/CL_0000000 denotes cell
T246 518-529 http://purl.obolibrary.org/obo/IDO_0000608 denotes replication
T247 620-624 http://purl.obolibrary.org/obo/CL_0000000 denotes cell
T248 756-764 http://purl.obolibrary.org/obo/IDO_0000528 denotes pathogen
T249 776-780 http://purl.obolibrary.org/obo/IDO_0000531 denotes host
T250 781-785 http://purl.obolibrary.org/obo/CL_0000000 denotes cell
T251 819-827 http://purl.obolibrary.org/obo/IDO_0000528 denotes pathogen
T252 843-851 http://purl.obolibrary.org/obo/IDO_0000528 denotes pathogen
T253 945-949 http://purl.obolibrary.org/obo/IDO_0000531 denotes host
T254 1270-1274 http://purl.obolibrary.org/obo/CL_0000000 denotes cell

LitCovid-sample-PD-FMA

Id Subject Object Predicate Lexical cue fma_id
T411 41-49 Body_part denotes cytokine http://purl.org/sig/ont/fma/fma84050
T412 226-231 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T413 241-266 Body_part denotes alveolar epithelial cells http://purl.org/sig/ont/fma/fma62499
T414 261-266 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T415 277-282 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T416 287-300 Body_part denotes immune system http://purl.org/sig/ont/fma/fma9825
T417 301-306 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T418 308-319 Body_part denotes macrophages http://purl.org/sig/ont/fma/fma63261
T419 321-330 Body_part denotes monocytes http://purl.org/sig/ont/fma/fma62864
T420 492-496 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T421 620-624 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T422 781-785 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T423 997-1004 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T424 1044-1051 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T425 1071-1078 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T426 1119-1126 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T427 1247-1256 Body_part denotes cytokines http://purl.org/sig/ont/fma/fma84050
T428 1270-1274 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646

LitCovid-sample-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T366 554-566 Disease denotes inflammation http://purl.obolibrary.org/obo/MONDO_0021166
T367 932-936 Disease denotes PRRs http://purl.obolibrary.org/obo/MONDO_0025494
T368 978-981 Disease denotes NOD http://purl.obolibrary.org/obo/MONDO_0007435
T369 1080-1083 Disease denotes ASC http://purl.obolibrary.org/obo/MONDO_0019018
T370 1294-1306 Disease denotes inflammation http://purl.obolibrary.org/obo/MONDO_0021166

LitCovid-sample-PD-GO-BP-0

Id Subject Object Predicate Lexical cue
T111 193-210 http://purl.obolibrary.org/obo/GO_0019058 denotes viral replication
T112 193-210 http://purl.obolibrary.org/obo/GO_0019079 denotes viral replication
T113 380-401 http://purl.obolibrary.org/obo/GO_0006954 denotes inflammatory response
T114 418-427 http://purl.obolibrary.org/obo/GO_0006915 denotes apoptosis
T115 418-427 http://purl.obolibrary.org/obo/GO_0097194 denotes apoptosis
T116 466-475 http://purl.obolibrary.org/obo/GO_0006915 denotes apoptosis
T117 466-475 http://purl.obolibrary.org/obo/GO_0097194 denotes apoptosis
T118 492-502 http://purl.obolibrary.org/obo/GO_0008219 denotes cell death
T119 497-502 http://purl.obolibrary.org/obo/GO_0016265 denotes death
T120 512-529 http://purl.obolibrary.org/obo/GO_0019058 denotes viral replication
T121 512-529 http://purl.obolibrary.org/obo/GO_0019079 denotes viral replication
T122 554-566 http://purl.obolibrary.org/obo/GO_0006954 denotes inflammation
T123 609-630 http://purl.obolibrary.org/obo/GO_0012501 denotes programmed cell death
T124 620-630 http://purl.obolibrary.org/obo/GO_0008219 denotes cell death
T125 625-630 http://purl.obolibrary.org/obo/GO_0016265 denotes death
T126 1052-1070 http://purl.obolibrary.org/obo/GO_0006919 denotes caspase activating
T127 1087-1096 http://purl.obolibrary.org/obo/GO_0006915 denotes apoptosis
T128 1087-1096 http://purl.obolibrary.org/obo/GO_0097194 denotes apoptosis
T129 1275-1280 http://purl.obolibrary.org/obo/GO_0019835 denotes lysis
T130 1294-1306 http://purl.obolibrary.org/obo/GO_0006954 denotes inflammation

LitCovid-sample-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T65 41-55 Phenotype denotes cytokine storm http://purl.obolibrary.org/obo/HP_0033041

LitCovid-sample-GO-BP

Id Subject Object Predicate Lexical cue
T111 193-210 http://purl.obolibrary.org/obo/GO_0019079 denotes viral replication
T112 193-210 http://purl.obolibrary.org/obo/GO_0019058 denotes viral replication
T113 380-401 http://purl.obolibrary.org/obo/GO_0006954 denotes inflammatory response
T114 418-427 http://purl.obolibrary.org/obo/GO_0097194 denotes apoptosis
T115 418-427 http://purl.obolibrary.org/obo/GO_0006915 denotes apoptosis
T116 432-442 http://purl.obolibrary.org/obo/GO_0070269 denotes pyroptosis
T117 466-475 http://purl.obolibrary.org/obo/GO_0097194 denotes apoptosis
T118 466-475 http://purl.obolibrary.org/obo/GO_0006915 denotes apoptosis
T119 492-502 http://purl.obolibrary.org/obo/GO_0008219 denotes cell death
T120 512-529 http://purl.obolibrary.org/obo/GO_0019079 denotes viral replication
T121 512-529 http://purl.obolibrary.org/obo/GO_0019058 denotes viral replication
T122 554-566 http://purl.obolibrary.org/obo/GO_0006954 denotes inflammation
T123 577-587 http://purl.obolibrary.org/obo/GO_0070269 denotes pyroptosis
T124 609-630 http://purl.obolibrary.org/obo/GO_0012501 denotes programmed cell death
T125 620-630 http://purl.obolibrary.org/obo/GO_0008219 denotes cell death
T126 729-739 http://purl.obolibrary.org/obo/GO_0070269 denotes pyroptosis
T127 1052-1070 http://purl.obolibrary.org/obo/GO_0006919 denotes caspase activating
T128 1087-1096 http://purl.obolibrary.org/obo/GO_0097194 denotes apoptosis
T129 1087-1096 http://purl.obolibrary.org/obo/GO_0006915 denotes apoptosis
T130 1275-1280 http://purl.obolibrary.org/obo/GO_0019835 denotes lysis
T131 1294-1306 http://purl.obolibrary.org/obo/GO_0006954 denotes inflammation

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T68 41-55 Phenotype denotes cytokine storm http://purl.obolibrary.org/obo/HP_0033041

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1725 72-76 Gene denotes ACE2 Gene:59272
1726 160-164 Gene denotes ACE2 Gene:59272
1727 1008-1013 Gene denotes NLRP3 Gene:114548
1728 1176-1185 Gene denotes caspase 1 Gene:834
1729 950-958 Gene denotes membrane Gene:43740571
1730 554-566 Disease denotes inflammation MESH:D007249
1731 1294-1306 Disease denotes inflammation MESH:D007249

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T373 0-118 Sentence denotes The molecular mechanisms involved in the cytokine storm and the role of ACE2 are currently still not fully understood.
T374 119-332 Sentence denotes As discussed above, virus binding to the ACE2 is the event that initiates viral replication in susceptible cells, such as alveolar epithelial cells, vascular cells and immune system cells (macrophages, monocytes).
T375 333-461 Sentence denotes This has been suggested to trigger the primary inflammatory response, which involves apoptosis and pyroptosis (Fu et al., 2020).
T376 462-712 Sentence denotes The apoptosis pattern indices cell death to avoid viral replication in the absence of overt inflammation, whereas, pyroptosis is a violent form of programmed cell death, followed by an inflammatory storm (Cookson and Brennan, 2001; Liu et al., 2016).
T377 713-959 Sentence denotes In the standard pyroptosis model, when the pathogen enters the host cell, some specific structures on the pathogen surface (PAMPs–pathogen associated molecular patterns) are identified by pattern recognition receptors (PRRs) on the host membrane.
T378 960-1405 Sentence denotes One common PRR is NOD-like receptors protein 3 (NLRP3), which forms together with a protein caspase activating protein (ASC or apoptosis-associated speck-like protein containing a caspase recruitment domain) and pro-caspase 1, the inflammasome unit capable of recruiting proinflammatory cytokines and inducing cell lysis with further inflammation signals (Fernandes-Alnemri et al., 2007; Schroder and Tschopp, 2010; Wree et al., 2014; Figure 9).